Shadow of Trouble
by Harem Master123
Summary: Atem has gone back to the Afterlife, but problems with the Shadow Realm have not disappeared. Portals to the Shadow Realm opening up in different places and causing new people problems. Yugi has decided to meet these people, join together, and defeat the Shadow Realm once and for all. Massive crossover
1. Beginning of Trouble! Yugi vs Yami Marik

AN This is a massive Yugioh crossover. I don't own any of the series that appear in this or any of the characters. I do own the idea of some original yugioh cards that appear here and now.

Yugi sighed as he sat in his room, typing away on his computer. It has been a few weeks since Yugi had defeated Atem and Atem passed onto the Afterlife. Yugi has been slightly relieved about this because they haven't had to deal with any Shadow Realm problems. Suddenly he heard a "Yugi!" from the window. While most would think it would be one of his friends, it was actually Serenity, Bakura, Seto, and Mai waiting for him. Ever since Atem left, Yugi's usual friends have avoided him because he looks so much like Atem. Yugi in his lonely state met up with Bakura who started to hang out with him. Serenity, who has transferred to Yugi's school, but a different grade, also began hanging out with them since Joey didn't like her being around Tristian. Since Seto couldn't stand Joey and always liked Yugi more than the other three also began hanging out with Yugi. Mai who had decided to stop travelling became a teacher at their school and started to hang out with Yugi and them. She tried to hang out with Joey, Tristian, and Tea but gave up after Joey started getting awkward around her.

Yugi smiled as he grabbed his duel disk, his deck, and his chain necklace with a small pyramid charm on it. He then proceeded to run out of the shop while yelling good bye to Solomon on his way out.

"Hey guys, sorry I was working on a report for school," Yugi apologized. Mai smirked at him and replied,"Well you should've started sooner on it." Yugi just playfully glared at her as he pointed his finger at her and yelled,"You're the one who assigned it to be 20 pages long. Who makes a high school student write a 20 page long paper!" Mai just chuckled as she patted Yugi's head making him huff. Seto just looked at this spectacle before looking down and noticing Yugi's duel disk.

"So I see you brought your duel disk. Planning to duel anybody?" Seto asked him in his usual serious voice. Yugi seemed to hear him as he turned around and nodded his head. Seto just smirked as he opened the suitcase he had and pulled out his own duel disk. "Was it me you were planning to duel because I've been itching to duel you for awhile," Seto said with one of his infamous Seto smirks. Yugi smiled as he took his deck out of his belt that held it, threw it into his duel disk, and turned it on. Seto responded by doing the same things.

"Let's duel!" they both yelled as they drew their cards.

As they began their duel they didn't notice shadows moving around them. Thankfully, Bakura who has been used to the Shadow Realm thanks to the spirit that was in him for so long using shadow powers so much saw the shadows. "Um guys I know you want to duel, but we have a problem!" Bakura yelled catching their attention. Seto looked over and saw a shadow jump at Serenity. Seto ran and tackled Serenity to the ground. Bakura grabbed Mai and moved her away from the area. Yugi deactivated his duel disk and was beginning to follow, but was stopped when he heard an all too familiar voice.

**"Yugi...where do you think you're going?"** Yugi heard coming from behind him. He turned around and saw someone that he thought that he and Atem got rid of along time ago. "Yami Marik!" Yugi yelled in fear. Yami Marik smirked as he nodded and put up his hand. Suddenly Yugi was trapped by an Egyptian God Slime that Yami Marik summoned. Yugi struggled, but soon felt his power disappear and felt his consciousness begin to leave him.

As the light almost left his eyes, he heard a voice. _"Yugi, you can do this!"_ Suddenly the Egyptian God Slime yelled in pain as it disappeared and Yugi stood there in a duel stance. "Yami Marik. I'm ready to get rid of you once and for all!" Yugi yelled.

_

Yami Marik chuckled as a duel disk formed on his arm. "Oh poor Yugi. Without the Pharoah, you have no chance against me. This will be a Shadow Game similar to the one your friend Joey had with me. You know, the one he lost," Yami Marik said with a smile on his face that enraged the small teen. Yugi drew five cards and then an extra one while yelling,"I'm first!"

Yugi scanned his hands looking for cards before spotting a few. "I lie a trap facedown and lay down Green Gadget in attack mode. And thanks to its effect I can get one Red Gadget from my deck and place it into my hand. I also lay down one more trap card and end my turn. Go demon," Yugi said as he glared at Yami Marik who just chuckled evilly before drawing a card and looking down at his hand.

**"I play Revival Jam in attack position and lay down three face downs. There I threw you a bone Yugi. Now show me what you are capable of without the Pharaoh's help,"** Yami Marik told Yugi as he ended his turn.

Yugi growled at him as he drew and saw that he had drawn Yellow Gadget. "Okay first I play Mystical Space Typhoon to destroy your middle face down!" Yugi yelled as a vortex came out and shattered the middle face down card on Yami Marik's side of the field, but he didn't look worried. "Now I play my new spell card, Double Summon to summon Yellow Gadget and Red Gadget! Now I activate my trap card, Stronghold the Moving Fortress. By adding these gadgets to it, it gets 3000 attack points! Now I attack your Jam!" Yugi yelled as the machine ran and smashed its fist into the jam causing it to be splattered everywhere before reforming making Yugi curse as he remembered that it could do that. Yugi noticed Yami Marik flinch so Yugi just looked at his hand and said,"I end my turn."

_Yugi: 4000_  
_Yami Marik: 2500_

Yami Marik just smirked as he drew and looked up at Yugi. **"I lay another facedown and play a trap facedown before switching Revival Jam to defense as well, go Yugi."** Yugi just glared before drawing another card and looking at his hand.

"I play Heavy Storm to destroy all traps and spell on the field, but my gadgets survive by separating from the fortress! Then I sacrifice one of them to summon Dark Magician Girl!" Yugi yelled as Red Gadget disappeared and Dark Magician Girl appeared. She turned around and waved at Yugi who smiled and waved back at her before looking back at Yami Marik. "I then attack your Revival Jam and thanks to it being in defense, it can't come back! Now go Dark Magician Girl, attack!" Yugi yelled as Dark Magician Girl charged Revival Jam. Suddenly Yami Marik smirked as he played a card. Yugi wasn't able to hear what card he played as he was defeaned by a loud yell.

"**My Man-Eater Bug just got one of your gadgets**," Yami Marik said with some cockiness in his voice. Yugi was shocked at the suddenness, but he then fell over and covered his mouth to keep from vomiting. "Yugi!" Dark Magician Girl yelled as she floated over to him. Yugi just smiled up at her while blood came out of his mouth before getting up. "I don't know what you did Yami Marik, but trust me...I'm not about to lose with so much on stake!" Yugi yelled as he played a Spell. "Reload, we put our hands into our deck and then draw the same amount back out," Yugi said as he put one card into his deck, shuffled the deck, and then drew.

"Now I play Dark Magic Curtain. I give up half my life points to Special Summon Dark Magician from my deck!" Yugi yelled as he grunted in pain as his life points dropped. Suddenly Dark Magician appeared next to Dark Magician Girl. "Now, Dark Magician, Dark Magic Attack!" Dark Magician shot a dark sphere out at Revival Jam, destroying it making Yami Marik glare slightly.

**"Hm...You are good Yugi, but still not good enough. Now watch as I end you!" **Yami Marik yelled as he drew.

_Yugi: 2000_  
_Yami Marik: 2500_

AN I hope you like this new fic, the pairings for it are just below this. Anyway, I would like if you gave me ideas for the kinds of decks the other main characters should have.

The main characters are: Yugi (Who will have a fusion of the deck he uses to duel Atem and Atem's deck), Negi (Negima), Keitaro (Love Hina), Keima (The World God Only Knows), Densuke (Eiken), Tsukune (Rosario+Vampire), Cody (Total Drama series), Danny (Danny Phantom), Peter (Ultimate Spiderman cartoon), Manaka (Ichigo 100%), Takeya (DearS), Yukinari (Girls Bravo), Taro (MM! or Emu Emu!), Chitose (Happy Lesson)

Pairings: Yugi/Ishizu  
Negi/Shizuna  
Keitaro/Haruka  
Keima/Nikaido (after they defeat the demon organization so she already knows that she's Dokuro)  
Densuke/Keiko  
Tsukune/Ageha  
Cody/Lindsay  
Danny/Desiree  
Peter/Ava  
Manaka/Shiori  
Takeya/Mitsuka  
Yukinari/Kirie  
Taro/Tomoko  
Chitose/Satsuki


	2. End of Duel!

AN Sorry for taking so long, but here's the next chapter and don't worry Cody's Children and Saiyan to Vampire soon.

I don't own Yu-Gi-Oh! or any anime/manga/cartoon featured in this fic

Chapter 2

Yugi felt his body weaken the longer he was stuck in the Shadow Realm with Yami Marik. It didn't help that he was coughing up blood every now and then. Yami Marik smirked as he looked at his hand. Yugi watched nervously, waiting for Yami Marik to make his move.

**"I play Monster Reborn to bring back Revival Jam in defense position and then I lay another monster facedown in defense position before ending my turn," **Yami Marik said calmly. Yugi looked at him suspiciously before drawing a card. Seeing that he only has one card in his hand now, he looked up at his field and saw that Yami Marik only had his two monsters on the field, but he wanted to play it safe.

"I lay one facedown and then I attack your facedown monster with Dark Magician Girl! Go!" Dark Magician stuck out her staff and shot a magic attack at the facedown monster. The monster flipped over and revealed itself to be a Cyber Jar making Yugi's eyes widen. "No!" Yugi yelled as the Cyber Jar's face went away and the jar started sucking in all the monsters on the field before exploding. Yami Marik laughed before drawing five cards with all five being monsters. **"I summon Holding Arms, Holding Legs, Makyura the Destructor, Dark Jeroid, and Drillago!" **Yami Marik yelled as all five monsters appeared on his side of the field while he smiled evilly at Yugi. Yugi growled as he drew five cards and was sad to see he only got two monsters. "I place the two monsters I drew in facedown defense position and lay down three facedowns," Yugi said as he ended his turn.

Yami Marik smirked as he drew before saying, **"Now I use my Holding Arms and Holding Legs to hold you in place!"** Yugi's eyes widened as the two monsters trapped him against an Egyptian looking wall. Yugi tried to move his arms and legs, but nothing was working causing him to curse as he remembered Mai's duel against him. **"Now Drillago attack his left defense monster!" **Drillago ran and smashed one of its drills into the monster. Unfortunately, it was Giant Soldier of Stone resulting in Yami Marik losing 400 life points.

_Yugi: 2000_  
_Yami Marik: 2100_

Yami Marik finally flinched in pain as the pain was finally getting to him. Yugi saw this and smirked seeing this, but Yami Marik saw him do this making Yami Marik just smirk back at him. Yugi then played a trap 'Ring of Destruction' and attached it to Drillago. **"I play Spell of Pain so now only you get the damage,"** Yami Marik said causing an invisible shield to appear, keeping him from getting hit by the ring's explosion. Yugi yelled in pain as he got hit by it.

_Yugi: 400_  
_Yami Marik: 2100_

**"I end my turn,"** Yami Marik spoke before looking away. Yugi knew he needed to draw a card, but thanks to Holding Arms, he couldn't move his arm to draw a card. Yugi moved his duel disk arm around as best as he could when suddenly his finger moved over a button he never noticed before. He pressed it with his finger of his left hand. Suddenly the top card of his deck shot out and into his right hand. "I play Monster Reborn to bring back Dark Magician from my graveyard and then I play-"Yugi looked at his hand and was shocked at what he saw._ "What...how did this get here?" _Yugi thought to himself.

**"Are you going to play whatever pathetic card or what?!"** Yami Marik yelled angrily. Yugi shook his head and then glared at an amused Yami Marik. Yugi through the card in his hand onto his duel disk. "-I summon the Eye of Timaeus! And now I use it's special effect to fuse it and Dark Magician to summon Amulet Dragon!" Yugi yelled as the two fused and then became Amulet Dragon. "Now I use Amulet Dragon's special effect. By removing all my spell cards in my graveyard from play and with each one it gains 300 attack points and I count six cards going away, that's a total of 1800 attack points, giving it 4500 attack points. Now Amulet Dragon! Attack Makyura!" Yugi yelled as Amulet Dragon shot a huge blast at it. Yami Marik growled as he realized he had nothing to defend himself with.

The attack hit Makyura and Yami Marik was sent flying back ten feet before smashing onto the ground and then puking up blood. The Holding Arms and Legs finally went away and Yugi fell to the ground in relief as his monsters disappeared. Yugi sighed before looking down at the Eye of Timaeus card. "Where did I get you from. I thought you left after the Atlantis fiasco?" he questioned before hearing chuckling. He looked up at Yami Marik who sat up and smiled at Yugi a very calm and reassuring smile.

**"Good Yugi, I knew you would win. It just took summoning that Atlantis dragon to do it,"** Yami Marik said. Yugi looked at him oddly before slowly walking over to him. "Yami Marik what are you talking about. Aren't you here to destroy me?" Yugi asked him.

**"Listen the Shadow Realm is opening portals everywhere because some mastermind is opening them. I know they are trying to find who they call the chosen ones and destroy them before they can stop them from destroying this world. I don't really like anybody here, but I know I tolerate you since you were the only one, other than the Pharaoh to come at me without fear. I'm going back to the Shadow Realm so try and stop them,"** Yami Marik told him as he looked at his body and saw it vanishing. Yugi listened to everything he said and then thought about something before making up his mind.

"I might regret this later, but I have my friends to help me if something bad happens," Yugi mumbled to himself before running over to Yami Marik's side, grabbed his shoulder, and started sucking Yami Marik into his pyramid charm. Yami Marik felt this and looked up at him strangely. **"What are you doing?"** Yami Marik asked him. Yugi smiled down at him and replied,"I figured that since you went out of your way to tell me this and test me to see if I was ready, you aren't as horrible as you were before and deserve a second chance. I'm going to let you reside in the charm before finding a way to free you."

**"You're still naive I can see. You sure you want to do this. I could turn on you later," **Yami Marik asked him. Yugi just nodded before Yami Marik vanished into his charm. Yugi sighed as he felt a new mental link open in his mind, taking the place of where Atem use to reside. Yugi sighed as he watched the Shadow Realm disappear and the real world come back.

He saw his friends looking at him with worry, but Yugi just smiled back at them and took a step before collapsing. Thankfully, Seto ran and caught him. "Yugi what happened in there?! You're bleeding!" Seto asked him with worry in his voice. Yugi just smiled at him and the others before replying,"I'll...tell...you when...I...wake...up." Yugi then fell unconscious. Seto quickly called for his limo to take him to his own personal hospital. Serenity, Bakura, and Mai left with them after leaving a note on Solomon's door explaining where Yugi was going.

_

_Unknown location_

A group of people walked into a room with a large statue of some monster that looked like a cross between Obelisk and Exodia. "So have you found the chosen ones?" the guy in front of the statue asked. One of the people who walked in bowed and said,"Sorry my master, but we have not found any of them because they haven't used a special card." Suddenly that guy was burnt to death in the blink of an eye. The 'Master' turned around and glared at the group causing them to flinch.

"Get out of here and go find them. Then destroy them," he said causing the group to nod and run out of the room. He then turned back to the statue and said,"I'm sorry my lord, but we will destroy those pesky chosen ones so they can't get in the way of your resurrection and then the destruction of Earth."

_**"Then hurry up and get more competent duelists and trackers so they can actually get rid of the chosen ones. The people you have now are so incompetent they couldn't win a duel with a beginner,"**_ a voice said causing the Master to nod his head and then pull out his phone to start making calls.

"It's just a matter of time before our lord is brought back and the Earth is destroyed. Get ready chosen ones, you're lives are about to end!" the Master yelled happily before the person he called picked up.

AN. I know this is a short chapter and I'm sorry, but this seemed like a good place to end the chapter. I know Yugi accepting to host Yami Marik in his body like he did for Atem seemed slightly out of character, but Yugi will be slightly OOC in this fic every now and then. Anyway we will be going to another character in the next chapter. Please review.


End file.
